diff --git a/CHANGELOG.md b/CHANGELOG.md index 5720af2f..09d6d600 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 1.5.2dev (UNRELEASED) + +## 1.5.1 + +### `Fixed` + +- [#253](https://github.com/nf-core/demultiplex/pull/253) Fixed mkfastq output channels. + ## 1.5.0 - 2024-08-12 ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5a5753e0..b88f8478 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,8 +1,8 @@ report_comment: > - This report has been generated by the nf-core/demultiplex + This report has been generated by the nf-core/demultiplex analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-demultiplex-methods-description": diff --git a/conf/modules.config b/conf/modules.config index e0d1c766..6d635d07 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -203,7 +203,14 @@ process { //Gather fastqs path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, - pattern: "**/outs/fastq_path/**.fastq.gz", + pattern: "**/outs/fastq_path/**/*.fastq.gz", + saveAs: {filename -> filename.split("/")[-1] } + ], + [ + //Gather undetermined fastqs + path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}/undetermined" : "${params.outdir}/${meta.id}/undetermined" }, + mode: params.publish_dir_mode, + pattern: "**/outs/fastq_path/*.fastq.gz", saveAs: {filename -> filename.split("/")[-1] } ] ] diff --git a/conf/test_mkfastq.config b/conf/test_mkfastq.config index 7990e1c8..7940f14d 100644 --- a/conf/test_mkfastq.config +++ b/conf/test_mkfastq.config @@ -20,7 +20,7 @@ params { max_time = '1.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/mkfastq-samplesheet.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/cellranger_tiny/mkfastq_tiny_samplesheet.csv' demultiplexer = 'mkfastq' - skip_tools = 'samshee' + skip_tools = 'samshee,falco' } diff --git a/modules.json b/modules.json index 2bf52fe9..8138d097 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "cellranger/mkfastq": { "branch": "master", - "git_sha": "d89faad13503f47372b8706008f7cdb2c4f1d859", + "git_sha": "61123e49c6034920eb6f312ad71e4815a7853257", "installed_by": ["modules"] }, "checkqc": { @@ -30,11 +30,6 @@ "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731", "installed_by": ["modules"] }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9", - "installed_by": ["modules"] - }, "falco": { "branch": "master", "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5", diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf index ab03f984..06c15bbc 100644 --- a/modules/nf-core/cellranger/mkfastq/main.nf +++ b/modules/nf-core/cellranger/mkfastq/main.nf @@ -8,11 +8,12 @@ process CELLRANGER_MKFASTQ { tuple val(meta), path(csv), path(bcl) output: - tuple val(meta), path("*_outs/outs/fastq_path/*.fastq.gz"), emit: fastq - tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports - tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats - tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop - path "versions.yml" , emit: versions + tuple val(meta), path("*_outs/outs/fastq_path/**/*.fastq.gz") , emit: fastq + tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz") , optional:true, emit: undetermined_fastq + tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports + tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats + tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -47,8 +48,8 @@ process CELLRANGER_MKFASTQ { } def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir -p "${prefix}_outs/outs/fastq_path/" - # data with something to avoid breaking nf-test java I/O stream + mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/" + # data with something to avoid breaking nf-test java I/O stream, fastq cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/fake_file.fastq @SEQ_ID GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT @@ -57,6 +58,15 @@ process CELLRANGER_MKFASTQ { FAKE_FQ gzip -n ${prefix}_outs/outs/fastq_path/fake_file.fastq + # data with something to avoid breaking nf-test java I/O stream, fastq_undetermined + cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq + @SEQ_ID + GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + + + !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 + FAKE_FQ + gzip -n ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq + # data for reports output channel mkdir -p "${prefix}_outs/outs/fastq_path/Reports" diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test index 8aee4001..8d3d718f 100644 --- a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test +++ b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test @@ -41,6 +41,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq, + process.out.undetermined_fastq, process.out.interop, process.out.versions ).match() @@ -65,6 +66,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq, + process.out.undetermined_fastq, process.out.interop, process.out.versions ).match() @@ -91,6 +93,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq, + process.out.undetermined_fastq, process.out.interop, process.out.versions ).match() diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap index e539f8e2..b1224688 100644 --- a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap @@ -1,6 +1,19 @@ { "cellranger - tiny - simple": { "content": [ + [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453", + "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc", + "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2" + ] + ] + ], [ [ { @@ -28,10 +41,10 @@ ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T20:45:20.493024717" + "timestamp": "2024-08-15T19:59:53.012035" }, "cellranger - tiny - simple - stub": { "content": [ @@ -43,6 +56,9 @@ }, "fake_file.fastq.gz:md5,8e16c1f4a441cbb3b7de374d2c924da7" ] + ], + [ + ], [ [ @@ -58,13 +74,26 @@ ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T20:47:11.995685118" + "timestamp": "2024-08-15T20:01:48.013075" }, "cellranger - tiny - illumina": { "content": [ + [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453", + "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc", + "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2" + ] + ] + ], [ [ { @@ -92,9 +121,9 @@ ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T20:46:17.031302052" + "timestamp": "2024-08-15T20:01:00.558148" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 61daeaf7..c018a819 100755 --- a/nextflow.config +++ b/nextflow.config @@ -275,7 +275,7 @@ manifest { description = """Demultiplexing pipeline for Illumina sequencing data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.5.0' + version = '1.5.1' doi = '10.5281/zenodo.7153103' } diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index 5d27853c..7b2399a1 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ b/tests/pipeline/bases2fastq.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{BASES2FASTQ={bases2fastq=1.8.0.1260801529, use subject to license available at elementbiosciences.com}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BASES2FASTQ={bases2fastq=1.8.0.1260801529, use subject to license available at elementbiosciences.com}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/pipeline/bcl2fastq.nf.test.snap b/tests/pipeline/bcl2fastq.nf.test.snap index 790585a1..cc26e2de 100644 --- a/tests/pipeline/bcl2fastq.nf.test.snap +++ b/tests/pipeline/bcl2fastq.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index 31d34736..49c9e7ab 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -28,7 +28,7 @@ }, "software_versions": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.8.4", diff --git a/tests/pipeline/fqtk.nf.test.snap b/tests/pipeline/fqtk.nf.test.snap index 61feca7a..5eace673 100644 --- a/tests/pipeline/fqtk.nf.test.snap +++ b/tests/pipeline/fqtk.nf.test.snap @@ -11,7 +11,7 @@ }, "software_versions": { "content": [ - "{CSV2TSV={sed=4.8}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{CSV2TSV={sed=4.8}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/pipeline/kraken.nf.test.snap b/tests/pipeline/kraken.nf.test.snap index 148712c2..acc440ac 100644 --- a/tests/pipeline/kraken.nf.test.snap +++ b/tests/pipeline/kraken.nf.test.snap @@ -63,7 +63,7 @@ }, "software_versions": { "content": [ - "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, KRAKEN2={kraken2=2.1.3, pigz=2.8}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, KRAKEN2={kraken2=2.1.3, pigz=2.8}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test index 885dff9e..584656b7 100644 --- a/tests/pipeline/mkfastq.nf.test +++ b/tests/pipeline/mkfastq.nf.test @@ -18,25 +18,32 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 7 }, + { assert workflow.trace.succeeded().size() == 10 }, // How many directories were produced? {assert path("${outputDir}").list().size() == 6}, // How many files were produced? - {assert path("$outputDir/220422_M11111_0222_000000000-K9H97_mkfastq/").list().size() == 2}, + {assert path("$outputDir/cellranger-tiny-bcl-simple/").list().size() == 2}, {assert path("$outputDir/multiqc/").list().size() == 3}, {assert path("$outputDir/pipeline_info/").list().size() == 5}, // File assertions: Files that should be exactly the same with every pipeline execution. {assert snapshot( //Check output files - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_summary.txt"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_report.html").exists(), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_R1_001.fastq.gz"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_fastqc_data.txt"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.json"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.html").exists(), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz.md5"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz"), - path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/InterOp/IndexMetricsOut.bin") + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz.md5"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz.md5"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz.md5"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R2_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_I1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"), + path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"), + path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin") ).match("file_assertions_mkfastq")} ) } diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap index d1d28977..0bbbb99e 100644 --- a/tests/pipeline/mkfastq.nf.test.snap +++ b/tests/pipeline/mkfastq.nf.test.snap @@ -1,30 +1,37 @@ { "software_versions": { "content": [ - "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.3" }, - "timestamp": "2024-08-02T20:09:53.707554042" + "timestamp": "2024-08-15T17:36:35.551329" }, "file_assertions_mkfastq": { "content": [ - "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6", + "test_sample_S1_L001_1.fastp.fastq.gz:md5,b348491a3b1afa096fde514dbdf55215", + "test_sample_S1_L001_1.fastp.fastq.gz.md5:md5,43d7882f3aaae47b56df56da6c802236", + "test_sample_S1_L001_2.fastp.fastq.gz:md5,1c60f1f3958b8b2b0255b9fae6df0b3d", + "test_sample_S1_L001_2.fastp.fastq.gz.md5:md5,01d742cc56639c476b0bac0c094eba4b", + "test_sample_S1_L001_I1_001.fastp.fastq.gz.md5:md5,82e397b4a2418f27269a30f6ca0e349e", + "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453", + "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc", + "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2", + "Undetermined_S0_L001_I1_001.fastq.gz:md5,c93946d67bdb1d5b2ab955fd1dc9cb31", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,faa79ce215ae72fdc3375cda066c6757", + "Undetermined_S0_L001_R2_001.fastq.gz:md5,d8955db4dfbf7aee89b6bdc3b7629f8f", true, - "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b", - "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7", - "Sample1_S1_L001.fastp.json:md5,ed62c667631b03f5fd3b50454322b423", true, - "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c", - "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373", - "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf" + "test_sample_S1_L001.fastp.json:md5,f616058446c5822797048ea6c5d2393d", + "test_sample_S1_L001_I1_001.fastp.json:md5,42cad4ed99a3d577f100017cbe11d711", + "IndexMetricsOut.bin:md5,e2ac28695537336b53a509f48e93ed1f" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-23T23:50:42.910185053" + "timestamp": "2024-08-15T17:54:45.551098" } } diff --git a/tests/pipeline/sgdemux.nf.test.snap b/tests/pipeline/sgdemux.nf.test.snap index 4f0b2a1c..28ee07a3 100644 --- a/tests/pipeline/sgdemux.nf.test.snap +++ b/tests/pipeline/sgdemux.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, SGDEMUX={sgdemux=1.1.1}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, SGDEMUX={sgdemux=1.1.1}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index 5416560a..40aa06d2 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions_skip_trimming": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", @@ -115,7 +115,7 @@ }, "software_versions_skip_fastqc": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", @@ -125,7 +125,7 @@ }, "software_versions_skip_fastp_fastqc": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", @@ -135,7 +135,7 @@ }, "software_versions_skip_multiqc": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", @@ -145,7 +145,7 @@ }, "software_versions_skip_fastp": { "content": [ - "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/pipeline/test_pe.nf.test.snap b/tests/pipeline/test_pe.nf.test.snap index 079f7fa9..fe9ecd36 100644 --- a/tests/pipeline/test_pe.nf.test.snap +++ b/tests/pipeline/test_pe.nf.test.snap @@ -66,7 +66,7 @@ }, "software_versions": { "content": [ - "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.0}}" + "{BCL2FASTQ={bcl2fastq=2.20.0.422}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" ], "meta": { "nf-test": "0.9.0",